Search for: All records

We describe approaches, results and insights from multi-year hackathons to enable their use in soft matter training and innovation. 

Abstract The cytoskeleton is an active composite of filamentous proteins that dictates diverse mechanical properties and processes in eukaryotic cells by generating forces and autonomously restructuring itself. Enzymatic motors that act on the comprising filaments play key roles in this activity, driving spatiotemporally heterogeneous mechanical responses that are critical to cellular multifunctionality, but also render mechanical characterization challenging. Here, we couple optical tweezers microrheology and fluorescence microscopy with simulations and mathematical modeling to robustly characterize the mechanics of active composites of actin filaments and microtubules restructured by kinesin motors. It is discovered that composites exhibit a rich ensemble of force response behaviors–elastic, yielding, and stiffening–with their propensity and properties tuned by motor concentration and strain rate. Moreover, intermediate kinesin concentrations elicit emergent mechanical stiffness and resistance while higher and lower concentrations exhibit softer, more viscous dissipation. It is further shown that composites transition from well‐mixed interpenetrating double‐networks of actin and microtubules to de‐mixed states of microtubule‐rich aggregates surrounded by relatively undisturbed actin phases. It is this de‐mixing that leads to the emergent mechanical response, offering an alternate route that composites can leverage to achieve enhanced stiffness through coupling of structure and mechanics. 

M13 phage are a novel microrheological probe that are sensitive to polymer relaxations, capturing DNA dynamics and revealing universal scaling behaviors across the unentangled and entangled regimes. 

The unique mechanical behaviors of actin–vimentin composites in both linear and nonlinear regimes are shaped by the complex interactions among actin entanglements, vimentin crosslinking, and poroelastic properties. 

The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments comprising the cytoskeleton often leads to anomalous subdiffusion, while active processes such as motor-driven restructuring can induce athermal superdiffusion. Understanding the interplay between these seemingly antagonistic contributions to intracellular dynamics remains a grand challenge. Here, we use single-molecule tracking to show that the transport of large linear and relaxed circular DNA through motor-driven microtubule networks can be non-Gaussian and multimodal, with the degree and spatiotemporal scales over which these features manifest depending nontrivially on the state of activity and DNA topology. For example, active network restructuring increases caging and non-Gaussian transport modes of linear DNA, while dampening these mechanisms for circular DNA. We further discover that circular DNA molecules exhibit either markedly enhanced subdiffusion or superdiffusion compared to their linear counterparts, in the absence or presence of kinesin activity, indicative of microtubules threading circular DNA. This strong coupling leads to both stalling and directed transport, providing a direct route towards parsing distinct contributions to transport and determining the impact of coupling on the transport signatures. More generally, leveraging macromolecular topology as a route to programming molecular interactions and transport dynamics is an elegant yet largely overlooked mechanism that cells may exploit for intracellular trafficking, streaming, and compartmentalization. This mechanism could be harnessed for the design of self-regulating, sensing, and reconfigurable biomimetic matter. Published by the American Physical Society2025 

Abstract DNA serves as a model system in polymer physics due to its ability to be obtained as a uniform polymer with controllable topology and non‐equilibrium behavior. Currently, a major obstacle in the widespread adoption of DNA is obtaining it on a scale and cost basis that accommodates bulk rheology and high‐throughput screening. To address this, recent advancements in bioreactor‐based plasmid DNA production is coupled with anion exchange chromatography to produce a unified approach to generating gram‐scale quantities of monodisperse DNA. With this method, 1.1 grams of DNA is obtained per batch to generate solutions with concentrations up to 116 mg mL⁻¹of uniform supercoiled and relaxed circular plasmid DNA, which is roughly 69 times greater than the overlap concentration. The utility of this method is demonstrated by performing bulk rheology measurements on DNA of different length, topologies, and concentrations at sample volumes up to 1 mL. The measured elastic moduli are orders of magnitude larger than those previously reported for DNA and allowed for the construction of a time‐concentration superposition curve that spans twelve decades of frequency. Ultimately, these results could provide important insights into the dynamics of ring polymers and the nature of highly condensed DNA dynamics. This article is protected by copyright. All rights reserved 

Polymer topology, which plays a principal role in the rheology of polymeric fluids, and non‐equilibrium materials, which exhibit time‐varying rheological properties, are topics of intense investigation. Here, composites of circular DNA and dextran are pushed out‐of‐equilibrium via enzymatic digestion of DNA rings to linear fragments. These time‐resolved rheology measurements reveal discrete state‐switching, with composites undergoing abrupt transitions between dissipative and elastic‐like states. The gating time and lifetime of the elastic‐like states, and the magnitude and sharpness of the transitions, are surprisingly decorrelated from digestion rates and non‐monotonically depend on the DNA fraction. These results are modeled using sigmoidal two‐state functions to show that bulk state‐switching can arise from continuous molecular‐level activity due to the necessity for cooperative percolation of entanglements to support macroscopic stresses. This platform, coupling the tunability of topological composites with the power of enzymatic reactions, may be leveraged for diverse material applications from wound‐healing to self‐repairing infrastructure.